Model has a hole in it due to weird geometry in wireframe mode?
You've created a shapekey and it is selected, so whenever you try to bring some corrections in Edit mode it changes this shapekey, not the base shapekey, and as soon as you come back to Object mode, you don't see what you've done on this second shapekey, as its value is at 0, you only see the base shapekey, which remains unchanged. So you need to select the base shapekey and work on it, you can even delete this second shapekey if it's not useful.